Thailand has sent around 1,300 Rohingya refugees back to Myanmar, a top official said Thursday, dismaying rights campaigners who warned the minority Muslims faced persecution in the former junta-ruled country.

Thousands of Rohingya, described by the United Nations as among the world's most persecuted minorities, have fled sectarian violence in western Myanmar in rickety boats since 2012, mostly heading for Malaysia.

Many of those who arrived in Thai waters were locked up in overcrowded immigration prisons.

Thai authorities began deporting the Rohingya in September through a border checkpoint in the province of Ranong, national immigration chief Lieutenant General Pharnu Kerdlarpphon told AFP news agency.

"The whole deportation process was completed in early November," he added.

It was the first official news of the deportation.

Rights activists criticised the move to return the Rohingya to Myanmar, where they face travel restrictions, forced labour and limited access to healthcare and education.

"The deportation of Rohingya is a blatant violation of international laws that prohibit sending back refugees and asylum-seekers to a place where they can face danger and persecution," said Sunai Phasuk, a senior researcher with New York-based Human Rights Watch.

Rights groups say the Rohingya often fall into the hands of people-traffickers, sometimes after they are deported by Thailand.

Mr Sunai urged the Thai authorities to explain what had happened to the 1,300 Rohingya, saying the foreign ministry did not appear to have been involved in the deportation.

There was no immediate comment from the ministry.

Thailand said last year it was investigating allegations that some army officials in the kingdom were involved in the trafficking of Rohingya.

Roughly 500 Rohingya are believed to remain in detention in Thailand following a raid on a suspected people-trafficking camp last month.

Myanmar views its population of roughly 800,000 Rohingya as illegal Bangladeshi immigrants and denies them citizenship.

More than 200 people have been killed and more than 140,000 left homeless in several outbreaks of Buddhist-Muslim violence since June 2012 in Myanmar's Rakhine state.

The United Nations has called on Myanmar to investigate reports -- denied by the authorities -- that dozens of men, women and children were killed in attacks on Rohingya last month with the alleged involvement of police.